Multiple sequence alignment - TraesCS1A01G196200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G196200 chr1A 100.000 3890 0 0 1 3890 354303644 354299755 0.000000e+00 7184.0
1 TraesCS1A01G196200 chr1D 96.806 3100 79 11 798 3890 282289342 282286256 0.000000e+00 5158.0
2 TraesCS1A01G196200 chr1D 93.548 186 11 1 1 186 282289857 282289673 3.830000e-70 276.0
3 TraesCS1A01G196200 chr1D 92.248 129 8 2 366 494 282289472 282289346 8.590000e-42 182.0
4 TraesCS1A01G196200 chr1B 95.747 2798 89 12 814 3601 383799994 383797217 0.000000e+00 4481.0
5 TraesCS1A01G196200 chr1B 95.156 289 6 3 3606 3890 383797166 383796882 2.130000e-122 449.0
6 TraesCS1A01G196200 chr1B 93.011 186 12 1 1 186 383800433 383800249 1.780000e-68 270.0
7 TraesCS1A01G196200 chr1B 95.192 104 4 1 394 497 383800120 383800018 3.110000e-36 163.0
8 TraesCS1A01G196200 chr2A 92.045 264 17 4 534 796 712296224 712295964 6.140000e-98 368.0
9 TraesCS1A01G196200 chr2A 93.200 250 16 1 548 796 17442397 17442148 2.210000e-97 366.0
10 TraesCS1A01G196200 chr5A 93.496 246 15 1 548 792 700868625 700868870 7.940000e-97 364.0
11 TraesCS1A01G196200 chr5A 94.000 50 0 2 495 544 594131906 594131952 5.390000e-09 73.1
12 TraesCS1A01G196200 chr5A 91.837 49 1 2 496 544 709483182 709483137 9.020000e-07 65.8
13 TraesCS1A01G196200 chr7B 93.443 244 15 1 548 790 200347402 200347645 1.030000e-95 361.0
14 TraesCS1A01G196200 chr5B 91.923 260 17 4 534 792 644946710 644946454 1.030000e-95 361.0
15 TraesCS1A01G196200 chr5B 86.441 59 4 3 486 544 641797762 641797708 1.170000e-05 62.1
16 TraesCS1A01G196200 chr2B 92.800 250 17 1 548 796 800099361 800099112 1.030000e-95 361.0
17 TraesCS1A01G196200 chr2B 89.655 58 1 3 489 544 106151589 106151535 6.970000e-08 69.4
18 TraesCS1A01G196200 chr3A 91.321 265 20 3 534 797 164275104 164275366 3.700000e-95 359.0
19 TraesCS1A01G196200 chr7A 90.977 266 20 3 548 812 106684355 106684093 4.780000e-94 355.0
20 TraesCS1A01G196200 chr7A 90.909 264 21 3 534 796 4502820 4502559 6.180000e-93 351.0
21 TraesCS1A01G196200 chr7A 90.741 54 1 3 491 544 516918219 516918170 6.970000e-08 69.4
22 TraesCS1A01G196200 chr6B 95.652 46 0 1 495 540 75916802 75916845 5.390000e-09 73.1
23 TraesCS1A01G196200 chr4A 93.878 49 0 2 496 544 595656331 595656376 1.940000e-08 71.3
24 TraesCS1A01G196200 chr4A 89.091 55 3 2 490 544 737298762 737298711 9.020000e-07 65.8
25 TraesCS1A01G196200 chr4B 88.525 61 1 5 488 545 561936303 561936360 6.970000e-08 69.4
26 TraesCS1A01G196200 chr3B 87.931 58 4 2 487 544 678449798 678449852 9.020000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G196200 chr1A 354299755 354303644 3889 True 7184.00 7184 100.000000 1 3890 1 chr1A.!!$R1 3889
1 TraesCS1A01G196200 chr1D 282286256 282289857 3601 True 1872.00 5158 94.200667 1 3890 3 chr1D.!!$R1 3889
2 TraesCS1A01G196200 chr1B 383796882 383800433 3551 True 1340.75 4481 94.776500 1 3890 4 chr1B.!!$R1 3889


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
338 390 0.249741 AGCACGTTTTAGCTGTCCGT 60.250 50.0 0.00 0.0 40.13 4.69 F
850 909 0.693049 GTTTCAGCCTCCTTCCTCCA 59.307 55.0 0.00 0.0 0.00 3.86 F
1683 1748 0.177141 GTACCATGGCCGAGCTACAA 59.823 55.0 13.04 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1747 0.742281 CGCATAGGACAGCAGCTGTT 60.742 55.000 28.84 16.67 45.44 3.16 R
1900 1965 1.303074 CGGATGCCATGGATCCCAG 60.303 63.158 25.39 15.33 36.75 4.45 R
3032 3097 0.537188 TTTTTGTTGGGCGCTTCCAA 59.463 45.000 13.35 13.35 43.82 3.53 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 4.722361 TCATTGCTAAGCATGCATCAAA 57.278 36.364 21.98 7.84 38.76 2.69
104 105 4.980434 GCTAAGCATGCATCAAATTCGATT 59.020 37.500 21.98 2.96 0.00 3.34
106 107 4.380841 AGCATGCATCAAATTCGATTGT 57.619 36.364 21.98 0.00 0.00 2.71
144 145 8.220559 ACCCAAAATGCAGTATCATACTCTATT 58.779 33.333 0.00 0.00 36.76 1.73
188 201 8.073768 AGATAAAACCATACAACTTTGACAACG 58.926 33.333 0.00 0.00 0.00 4.10
194 207 3.111958 ACAACTTTGACAACGACAACG 57.888 42.857 0.00 0.00 45.75 4.10
195 208 1.837747 CAACTTTGACAACGACAACGC 59.162 47.619 0.00 0.00 43.96 4.84
209 222 2.902484 GACAACGCAGCATTTAGTTTCG 59.098 45.455 0.00 0.00 0.00 3.46
213 226 2.157668 ACGCAGCATTTAGTTTCGACTG 59.842 45.455 0.00 0.00 0.00 3.51
215 228 2.729156 GCAGCATTTAGTTTCGACTGGC 60.729 50.000 0.00 0.00 0.00 4.85
219 239 3.933332 GCATTTAGTTTCGACTGGCTAGT 59.067 43.478 0.69 0.69 40.66 2.57
259 279 9.821240 ATTTATGGTTTTGGTATATGGATAGCA 57.179 29.630 0.00 0.00 42.82 3.49
270 290 7.040478 TGGTATATGGATAGCAAGTTTTCATGC 60.040 37.037 0.00 0.00 41.84 4.06
271 291 6.964807 ATATGGATAGCAAGTTTTCATGCA 57.035 33.333 0.00 0.00 45.49 3.96
272 292 5.864418 ATGGATAGCAAGTTTTCATGCAT 57.136 34.783 0.00 0.00 45.49 3.96
273 293 5.252969 TGGATAGCAAGTTTTCATGCATC 57.747 39.130 0.00 2.12 45.49 3.91
274 294 4.098349 TGGATAGCAAGTTTTCATGCATCC 59.902 41.667 0.00 15.80 45.49 3.51
275 295 4.500375 GGATAGCAAGTTTTCATGCATCCC 60.500 45.833 0.00 3.60 45.49 3.85
283 335 4.159135 AGTTTTCATGCATCCCTTCATGTC 59.841 41.667 0.00 0.00 40.54 3.06
293 345 5.797051 CATCCCTTCATGTCAAATTTGGTT 58.203 37.500 17.90 0.89 0.00 3.67
294 346 5.467035 TCCCTTCATGTCAAATTTGGTTC 57.533 39.130 17.90 9.52 0.00 3.62
318 370 9.627123 TTCATCCCGAACTTTCTTGATATTATT 57.373 29.630 0.00 0.00 0.00 1.40
324 376 8.004344 CCGAACTTTCTTGATATTATTAGCACG 58.996 37.037 0.00 0.00 0.00 5.34
325 377 8.540492 CGAACTTTCTTGATATTATTAGCACGT 58.460 33.333 0.00 0.00 0.00 4.49
332 384 9.542462 TCTTGATATTATTAGCACGTTTTAGCT 57.458 29.630 3.45 3.45 44.55 3.32
335 387 8.761497 TGATATTATTAGCACGTTTTAGCTGTC 58.239 33.333 8.27 0.00 41.97 3.51
338 390 0.249741 AGCACGTTTTAGCTGTCCGT 60.250 50.000 0.00 0.00 40.13 4.69
343 395 3.430895 CACGTTTTAGCTGTCCGTTATGT 59.569 43.478 0.00 0.00 0.00 2.29
345 397 4.622740 ACGTTTTAGCTGTCCGTTATGTAC 59.377 41.667 0.00 0.00 0.00 2.90
346 398 4.860907 CGTTTTAGCTGTCCGTTATGTACT 59.139 41.667 0.00 0.00 0.00 2.73
347 399 5.220154 CGTTTTAGCTGTCCGTTATGTACTG 60.220 44.000 0.00 0.00 0.00 2.74
348 400 5.648178 TTTAGCTGTCCGTTATGTACTGA 57.352 39.130 0.00 0.00 0.00 3.41
349 401 5.648178 TTAGCTGTCCGTTATGTACTGAA 57.352 39.130 0.00 0.00 0.00 3.02
350 402 4.530710 AGCTGTCCGTTATGTACTGAAA 57.469 40.909 0.00 0.00 0.00 2.69
351 403 5.086104 AGCTGTCCGTTATGTACTGAAAT 57.914 39.130 0.00 0.00 0.00 2.17
352 404 5.488341 AGCTGTCCGTTATGTACTGAAATT 58.512 37.500 0.00 0.00 0.00 1.82
353 405 5.938125 AGCTGTCCGTTATGTACTGAAATTT 59.062 36.000 0.00 0.00 0.00 1.82
354 406 7.101054 AGCTGTCCGTTATGTACTGAAATTTA 58.899 34.615 0.00 0.00 0.00 1.40
357 409 9.093970 CTGTCCGTTATGTACTGAAATTTATGA 57.906 33.333 0.00 0.00 0.00 2.15
362 414 8.612619 CGTTATGTACTGAAATTTATGAAGGCT 58.387 33.333 0.00 0.00 0.00 4.58
382 434 5.129155 AGGCTTGCATTGAATATGCCTAAAA 59.871 36.000 5.78 0.00 46.10 1.52
386 438 7.011669 GCTTGCATTGAATATGCCTAAAACATT 59.988 33.333 7.23 0.00 43.94 2.71
494 546 8.352942 GTCCAGACAGTCAAAAGAAAATGTTAT 58.647 33.333 2.66 0.00 0.00 1.89
495 547 8.912988 TCCAGACAGTCAAAAGAAAATGTTATT 58.087 29.630 2.66 0.00 0.00 1.40
508 560 8.451908 AGAAAATGTTATTACTATGAGGGTGC 57.548 34.615 0.00 0.00 0.00 5.01
509 561 8.275040 AGAAAATGTTATTACTATGAGGGTGCT 58.725 33.333 0.00 0.00 0.00 4.40
510 562 8.823220 AAAATGTTATTACTATGAGGGTGCTT 57.177 30.769 0.00 0.00 0.00 3.91
511 563 7.807977 AATGTTATTACTATGAGGGTGCTTG 57.192 36.000 0.00 0.00 0.00 4.01
512 564 5.680619 TGTTATTACTATGAGGGTGCTTGG 58.319 41.667 0.00 0.00 0.00 3.61
513 565 5.427157 TGTTATTACTATGAGGGTGCTTGGA 59.573 40.000 0.00 0.00 0.00 3.53
514 566 6.101150 TGTTATTACTATGAGGGTGCTTGGAT 59.899 38.462 0.00 0.00 0.00 3.41
515 567 7.291416 TGTTATTACTATGAGGGTGCTTGGATA 59.709 37.037 0.00 0.00 0.00 2.59
516 568 5.546621 TTACTATGAGGGTGCTTGGATAC 57.453 43.478 0.00 0.00 0.00 2.24
517 569 2.365617 ACTATGAGGGTGCTTGGATACG 59.634 50.000 0.00 0.00 42.51 3.06
518 570 1.204146 ATGAGGGTGCTTGGATACGT 58.796 50.000 0.00 0.00 42.51 3.57
519 571 0.981183 TGAGGGTGCTTGGATACGTT 59.019 50.000 0.00 0.00 42.51 3.99
520 572 1.349688 TGAGGGTGCTTGGATACGTTT 59.650 47.619 0.00 0.00 42.51 3.60
521 573 2.224670 TGAGGGTGCTTGGATACGTTTT 60.225 45.455 0.00 0.00 42.51 2.43
522 574 3.008157 TGAGGGTGCTTGGATACGTTTTA 59.992 43.478 0.00 0.00 42.51 1.52
523 575 3.606687 AGGGTGCTTGGATACGTTTTAG 58.393 45.455 0.00 0.00 42.51 1.85
524 576 3.008704 AGGGTGCTTGGATACGTTTTAGT 59.991 43.478 0.00 0.00 42.51 2.24
525 577 3.373130 GGGTGCTTGGATACGTTTTAGTC 59.627 47.826 0.00 0.00 42.51 2.59
526 578 3.373130 GGTGCTTGGATACGTTTTAGTCC 59.627 47.826 0.00 0.00 42.51 3.85
527 579 3.373130 GTGCTTGGATACGTTTTAGTCCC 59.627 47.826 0.00 0.00 42.51 4.46
528 580 3.008157 TGCTTGGATACGTTTTAGTCCCA 59.992 43.478 0.00 0.00 42.51 4.37
529 581 4.196971 GCTTGGATACGTTTTAGTCCCAT 58.803 43.478 0.00 0.00 42.51 4.00
530 582 4.035208 GCTTGGATACGTTTTAGTCCCATG 59.965 45.833 0.00 0.00 42.51 3.66
531 583 4.145365 TGGATACGTTTTAGTCCCATGG 57.855 45.455 4.14 4.14 42.51 3.66
532 584 3.118186 TGGATACGTTTTAGTCCCATGGG 60.118 47.826 26.30 26.30 42.51 4.00
533 585 3.135167 GGATACGTTTTAGTCCCATGGGA 59.865 47.826 30.62 30.62 42.90 4.37
545 597 4.411256 TCCCATGGGACTAAAACGTATC 57.589 45.455 30.62 0.00 39.76 2.24
546 598 3.135167 TCCCATGGGACTAAAACGTATCC 59.865 47.826 30.62 0.00 39.76 2.59
547 599 3.118186 CCCATGGGACTAAAACGTATCCA 60.118 47.826 28.27 0.00 37.50 3.41
548 600 4.519213 CCATGGGACTAAAACGTATCCAA 58.481 43.478 2.85 0.00 32.45 3.53
549 601 4.944930 CCATGGGACTAAAACGTATCCAAA 59.055 41.667 2.85 0.00 32.45 3.28
550 602 5.416326 CCATGGGACTAAAACGTATCCAAAA 59.584 40.000 2.85 0.00 32.45 2.44
551 603 6.096282 CCATGGGACTAAAACGTATCCAAAAT 59.904 38.462 2.85 0.00 32.45 1.82
552 604 6.746745 TGGGACTAAAACGTATCCAAAATC 57.253 37.500 0.00 0.00 32.45 2.17
553 605 6.239396 TGGGACTAAAACGTATCCAAAATCA 58.761 36.000 0.00 0.00 32.45 2.57
554 606 6.715718 TGGGACTAAAACGTATCCAAAATCAA 59.284 34.615 0.00 0.00 32.45 2.57
555 607 7.094549 TGGGACTAAAACGTATCCAAAATCAAG 60.095 37.037 0.00 0.00 32.45 3.02
556 608 7.094506 GGGACTAAAACGTATCCAAAATCAAGT 60.095 37.037 0.00 0.00 32.45 3.16
557 609 8.294577 GGACTAAAACGTATCCAAAATCAAGTT 58.705 33.333 0.00 0.00 0.00 2.66
584 636 7.346751 TGAGCATTTATTATCCTTCAAACCC 57.653 36.000 0.00 0.00 0.00 4.11
585 637 7.125391 TGAGCATTTATTATCCTTCAAACCCT 58.875 34.615 0.00 0.00 0.00 4.34
586 638 7.619302 TGAGCATTTATTATCCTTCAAACCCTT 59.381 33.333 0.00 0.00 0.00 3.95
587 639 8.011844 AGCATTTATTATCCTTCAAACCCTTC 57.988 34.615 0.00 0.00 0.00 3.46
588 640 7.619302 AGCATTTATTATCCTTCAAACCCTTCA 59.381 33.333 0.00 0.00 0.00 3.02
589 641 8.257306 GCATTTATTATCCTTCAAACCCTTCAA 58.743 33.333 0.00 0.00 0.00 2.69
592 644 9.768215 TTTATTATCCTTCAAACCCTTCAATCT 57.232 29.630 0.00 0.00 0.00 2.40
594 646 8.986929 ATTATCCTTCAAACCCTTCAATCTAG 57.013 34.615 0.00 0.00 0.00 2.43
595 647 6.642733 ATCCTTCAAACCCTTCAATCTAGA 57.357 37.500 0.00 0.00 0.00 2.43
596 648 6.448369 TCCTTCAAACCCTTCAATCTAGAA 57.552 37.500 0.00 0.00 0.00 2.10
597 649 6.238648 TCCTTCAAACCCTTCAATCTAGAAC 58.761 40.000 0.00 0.00 0.00 3.01
598 650 6.044404 TCCTTCAAACCCTTCAATCTAGAACT 59.956 38.462 0.00 0.00 0.00 3.01
599 651 6.372937 CCTTCAAACCCTTCAATCTAGAACTC 59.627 42.308 0.00 0.00 0.00 3.01
600 652 5.479306 TCAAACCCTTCAATCTAGAACTCG 58.521 41.667 0.00 0.00 0.00 4.18
601 653 3.528597 ACCCTTCAATCTAGAACTCGC 57.471 47.619 0.00 0.00 0.00 5.03
602 654 2.832129 ACCCTTCAATCTAGAACTCGCA 59.168 45.455 0.00 0.00 0.00 5.10
603 655 3.452627 ACCCTTCAATCTAGAACTCGCAT 59.547 43.478 0.00 0.00 0.00 4.73
604 656 3.806521 CCCTTCAATCTAGAACTCGCATG 59.193 47.826 0.00 0.00 0.00 4.06
605 657 4.437239 CCTTCAATCTAGAACTCGCATGT 58.563 43.478 0.00 0.00 0.00 3.21
606 658 4.269603 CCTTCAATCTAGAACTCGCATGTG 59.730 45.833 0.00 0.00 0.00 3.21
607 659 4.456280 TCAATCTAGAACTCGCATGTGT 57.544 40.909 6.09 0.00 0.00 3.72
608 660 4.820897 TCAATCTAGAACTCGCATGTGTT 58.179 39.130 6.09 3.50 34.68 3.32
609 661 5.961272 TCAATCTAGAACTCGCATGTGTTA 58.039 37.500 6.09 0.00 32.29 2.41
610 662 6.394809 TCAATCTAGAACTCGCATGTGTTAA 58.605 36.000 6.09 0.00 32.29 2.01
611 663 6.871492 TCAATCTAGAACTCGCATGTGTTAAA 59.129 34.615 6.09 0.00 32.29 1.52
612 664 6.893958 ATCTAGAACTCGCATGTGTTAAAG 57.106 37.500 6.09 0.00 32.29 1.85
613 665 6.020971 TCTAGAACTCGCATGTGTTAAAGA 57.979 37.500 6.09 6.98 32.29 2.52
614 666 6.452242 TCTAGAACTCGCATGTGTTAAAGAA 58.548 36.000 6.09 0.00 32.29 2.52
615 667 5.597813 AGAACTCGCATGTGTTAAAGAAG 57.402 39.130 6.09 0.00 32.29 2.85
616 668 5.297547 AGAACTCGCATGTGTTAAAGAAGA 58.702 37.500 6.09 0.00 32.29 2.87
617 669 5.406780 AGAACTCGCATGTGTTAAAGAAGAG 59.593 40.000 6.09 0.00 32.29 2.85
618 670 3.997021 ACTCGCATGTGTTAAAGAAGAGG 59.003 43.478 6.09 0.00 0.00 3.69
619 671 2.742053 TCGCATGTGTTAAAGAAGAGGC 59.258 45.455 6.09 0.00 0.00 4.70
620 672 2.483877 CGCATGTGTTAAAGAAGAGGCA 59.516 45.455 0.00 0.00 0.00 4.75
621 673 3.127548 CGCATGTGTTAAAGAAGAGGCAT 59.872 43.478 0.00 0.00 0.00 4.40
622 674 4.379813 CGCATGTGTTAAAGAAGAGGCATT 60.380 41.667 0.00 0.00 0.00 3.56
623 675 5.163764 CGCATGTGTTAAAGAAGAGGCATTA 60.164 40.000 0.00 0.00 0.00 1.90
624 676 6.620678 GCATGTGTTAAAGAAGAGGCATTAA 58.379 36.000 0.00 0.00 0.00 1.40
625 677 7.090173 GCATGTGTTAAAGAAGAGGCATTAAA 58.910 34.615 0.00 0.00 0.00 1.52
626 678 7.761249 GCATGTGTTAAAGAAGAGGCATTAAAT 59.239 33.333 0.00 0.00 0.00 1.40
627 679 9.079833 CATGTGTTAAAGAAGAGGCATTAAATG 57.920 33.333 0.00 0.00 0.00 2.32
628 680 8.402798 TGTGTTAAAGAAGAGGCATTAAATGA 57.597 30.769 0.00 0.00 0.00 2.57
629 681 9.023962 TGTGTTAAAGAAGAGGCATTAAATGAT 57.976 29.630 0.00 0.00 0.00 2.45
630 682 9.294030 GTGTTAAAGAAGAGGCATTAAATGATG 57.706 33.333 0.00 0.00 0.00 3.07
631 683 9.241919 TGTTAAAGAAGAGGCATTAAATGATGA 57.758 29.630 0.00 0.00 0.00 2.92
632 684 9.727627 GTTAAAGAAGAGGCATTAAATGATGAG 57.272 33.333 0.00 0.00 0.00 2.90
633 685 9.685276 TTAAAGAAGAGGCATTAAATGATGAGA 57.315 29.630 0.00 0.00 0.00 3.27
634 686 7.804843 AAGAAGAGGCATTAAATGATGAGAG 57.195 36.000 0.00 0.00 0.00 3.20
635 687 7.134362 AGAAGAGGCATTAAATGATGAGAGA 57.866 36.000 0.00 0.00 0.00 3.10
636 688 7.218614 AGAAGAGGCATTAAATGATGAGAGAG 58.781 38.462 0.00 0.00 0.00 3.20
637 689 6.744175 AGAGGCATTAAATGATGAGAGAGA 57.256 37.500 0.00 0.00 0.00 3.10
638 690 6.761312 AGAGGCATTAAATGATGAGAGAGAG 58.239 40.000 0.00 0.00 0.00 3.20
639 691 5.867330 AGGCATTAAATGATGAGAGAGAGG 58.133 41.667 0.00 0.00 0.00 3.69
640 692 5.002516 GGCATTAAATGATGAGAGAGAGGG 58.997 45.833 0.00 0.00 0.00 4.30
641 693 4.455190 GCATTAAATGATGAGAGAGAGGGC 59.545 45.833 0.00 0.00 0.00 5.19
642 694 5.745476 GCATTAAATGATGAGAGAGAGGGCT 60.745 44.000 0.00 0.00 0.00 5.19
643 695 6.519721 GCATTAAATGATGAGAGAGAGGGCTA 60.520 42.308 0.00 0.00 0.00 3.93
644 696 7.448420 CATTAAATGATGAGAGAGAGGGCTAA 58.552 38.462 0.00 0.00 0.00 3.09
645 697 7.623999 TTAAATGATGAGAGAGAGGGCTAAT 57.376 36.000 0.00 0.00 0.00 1.73
646 698 8.727100 TTAAATGATGAGAGAGAGGGCTAATA 57.273 34.615 0.00 0.00 0.00 0.98
647 699 6.603940 AATGATGAGAGAGAGGGCTAATAC 57.396 41.667 0.00 0.00 0.00 1.89
648 700 5.066913 TGATGAGAGAGAGGGCTAATACA 57.933 43.478 0.00 0.00 0.00 2.29
649 701 5.649265 TGATGAGAGAGAGGGCTAATACAT 58.351 41.667 0.00 0.00 0.00 2.29
650 702 6.794534 TGATGAGAGAGAGGGCTAATACATA 58.205 40.000 0.00 0.00 0.00 2.29
651 703 7.417554 TGATGAGAGAGAGGGCTAATACATAT 58.582 38.462 0.00 0.00 0.00 1.78
652 704 7.898100 TGATGAGAGAGAGGGCTAATACATATT 59.102 37.037 0.00 0.00 0.00 1.28
653 705 8.677870 ATGAGAGAGAGGGCTAATACATATTT 57.322 34.615 0.00 0.00 0.00 1.40
654 706 8.497910 TGAGAGAGAGGGCTAATACATATTTT 57.502 34.615 0.00 0.00 0.00 1.82
655 707 9.601810 TGAGAGAGAGGGCTAATACATATTTTA 57.398 33.333 0.00 0.00 0.00 1.52
657 709 9.608718 AGAGAGAGGGCTAATACATATTTTAGT 57.391 33.333 0.00 0.00 0.00 2.24
700 752 8.478775 AAAATTTTAGCCTCAAAACTAGTCCT 57.521 30.769 0.37 0.00 30.57 3.85
701 753 9.582648 AAAATTTTAGCCTCAAAACTAGTCCTA 57.417 29.630 0.37 0.00 30.57 2.94
702 754 8.794335 AATTTTAGCCTCAAAACTAGTCCTAG 57.206 34.615 0.00 0.00 39.04 3.02
703 755 3.897141 AGCCTCAAAACTAGTCCTAGC 57.103 47.619 0.00 0.00 36.66 3.42
704 756 2.502130 AGCCTCAAAACTAGTCCTAGCC 59.498 50.000 0.00 0.00 36.66 3.93
705 757 2.502130 GCCTCAAAACTAGTCCTAGCCT 59.498 50.000 0.00 0.00 36.66 4.58
706 758 3.431068 GCCTCAAAACTAGTCCTAGCCTC 60.431 52.174 0.00 0.00 36.66 4.70
707 759 4.027437 CCTCAAAACTAGTCCTAGCCTCT 58.973 47.826 0.00 0.00 36.66 3.69
708 760 4.098807 CCTCAAAACTAGTCCTAGCCTCTC 59.901 50.000 0.00 0.00 36.66 3.20
709 761 4.936802 TCAAAACTAGTCCTAGCCTCTCT 58.063 43.478 0.00 0.00 36.66 3.10
710 762 5.334421 TCAAAACTAGTCCTAGCCTCTCTT 58.666 41.667 0.00 0.00 36.66 2.85
711 763 5.780793 TCAAAACTAGTCCTAGCCTCTCTTT 59.219 40.000 0.00 0.00 36.66 2.52
712 764 6.952358 TCAAAACTAGTCCTAGCCTCTCTTTA 59.048 38.462 0.00 0.00 36.66 1.85
713 765 7.122948 TCAAAACTAGTCCTAGCCTCTCTTTAG 59.877 40.741 0.00 0.00 36.66 1.85
714 766 5.720486 ACTAGTCCTAGCCTCTCTTTAGT 57.280 43.478 1.22 0.00 36.66 2.24
715 767 5.687780 ACTAGTCCTAGCCTCTCTTTAGTC 58.312 45.833 1.22 0.00 36.66 2.59
716 768 4.594675 AGTCCTAGCCTCTCTTTAGTCA 57.405 45.455 0.00 0.00 0.00 3.41
717 769 4.532834 AGTCCTAGCCTCTCTTTAGTCAG 58.467 47.826 0.00 0.00 0.00 3.51
718 770 3.634910 GTCCTAGCCTCTCTTTAGTCAGG 59.365 52.174 0.00 0.00 0.00 3.86
719 771 3.528078 TCCTAGCCTCTCTTTAGTCAGGA 59.472 47.826 0.00 0.00 0.00 3.86
720 772 3.888930 CCTAGCCTCTCTTTAGTCAGGAG 59.111 52.174 0.00 0.00 0.00 3.69
721 773 3.466395 AGCCTCTCTTTAGTCAGGAGT 57.534 47.619 0.00 0.00 0.00 3.85
722 774 3.096092 AGCCTCTCTTTAGTCAGGAGTG 58.904 50.000 0.00 0.00 0.00 3.51
723 775 2.418060 GCCTCTCTTTAGTCAGGAGTGC 60.418 54.545 0.00 0.00 0.00 4.40
724 776 3.096092 CCTCTCTTTAGTCAGGAGTGCT 58.904 50.000 0.00 0.00 0.00 4.40
725 777 3.513515 CCTCTCTTTAGTCAGGAGTGCTT 59.486 47.826 0.00 0.00 0.00 3.91
726 778 4.493547 CTCTCTTTAGTCAGGAGTGCTTG 58.506 47.826 0.00 0.00 0.00 4.01
727 779 4.152647 TCTCTTTAGTCAGGAGTGCTTGA 58.847 43.478 0.00 0.00 0.00 3.02
728 780 4.588951 TCTCTTTAGTCAGGAGTGCTTGAA 59.411 41.667 0.00 0.00 31.41 2.69
729 781 5.070446 TCTCTTTAGTCAGGAGTGCTTGAAA 59.930 40.000 0.00 0.00 31.41 2.69
730 782 5.057149 TCTTTAGTCAGGAGTGCTTGAAAC 58.943 41.667 0.00 0.00 31.41 2.78
731 783 4.689612 TTAGTCAGGAGTGCTTGAAACT 57.310 40.909 0.00 0.00 31.41 2.66
732 784 3.567478 AGTCAGGAGTGCTTGAAACTT 57.433 42.857 0.00 0.00 31.41 2.66
733 785 3.891049 AGTCAGGAGTGCTTGAAACTTT 58.109 40.909 0.00 0.00 31.41 2.66
734 786 5.036117 AGTCAGGAGTGCTTGAAACTTTA 57.964 39.130 0.00 0.00 31.41 1.85
735 787 5.059833 AGTCAGGAGTGCTTGAAACTTTAG 58.940 41.667 0.00 0.00 31.41 1.85
736 788 4.816925 GTCAGGAGTGCTTGAAACTTTAGT 59.183 41.667 0.00 0.00 31.41 2.24
737 789 5.050023 GTCAGGAGTGCTTGAAACTTTAGTC 60.050 44.000 0.00 0.00 31.41 2.59
738 790 5.059833 CAGGAGTGCTTGAAACTTTAGTCT 58.940 41.667 0.00 0.00 0.00 3.24
739 791 5.529060 CAGGAGTGCTTGAAACTTTAGTCTT 59.471 40.000 0.00 0.00 0.00 3.01
740 792 6.038714 CAGGAGTGCTTGAAACTTTAGTCTTT 59.961 38.462 0.00 0.00 0.00 2.52
741 793 7.226720 CAGGAGTGCTTGAAACTTTAGTCTTTA 59.773 37.037 0.00 0.00 0.00 1.85
742 794 7.773690 AGGAGTGCTTGAAACTTTAGTCTTTAA 59.226 33.333 0.00 0.00 0.00 1.52
743 795 8.403236 GGAGTGCTTGAAACTTTAGTCTTTAAA 58.597 33.333 0.00 0.00 0.00 1.52
744 796 9.783256 GAGTGCTTGAAACTTTAGTCTTTAAAA 57.217 29.630 0.00 0.00 0.00 1.52
783 835 9.981460 AATCAGACTAAAAATAGTCCTTTGGAT 57.019 29.630 11.35 5.94 45.66 3.41
784 836 9.620259 ATCAGACTAAAAATAGTCCTTTGGATC 57.380 33.333 11.35 0.00 45.66 3.36
785 837 8.602424 TCAGACTAAAAATAGTCCTTTGGATCA 58.398 33.333 11.35 0.00 45.66 2.92
786 838 9.231297 CAGACTAAAAATAGTCCTTTGGATCAA 57.769 33.333 11.35 0.00 45.66 2.57
787 839 9.454859 AGACTAAAAATAGTCCTTTGGATCAAG 57.545 33.333 11.35 0.00 45.66 3.02
788 840 8.056407 ACTAAAAATAGTCCTTTGGATCAAGC 57.944 34.615 0.00 0.00 32.73 4.01
789 841 6.916360 AAAAATAGTCCTTTGGATCAAGCA 57.084 33.333 0.00 0.00 32.73 3.91
790 842 5.904362 AAATAGTCCTTTGGATCAAGCAC 57.096 39.130 0.00 0.00 32.73 4.40
791 843 2.206576 AGTCCTTTGGATCAAGCACC 57.793 50.000 0.00 0.00 32.73 5.01
792 844 1.707427 AGTCCTTTGGATCAAGCACCT 59.293 47.619 0.00 0.00 32.73 4.00
793 845 2.108952 AGTCCTTTGGATCAAGCACCTT 59.891 45.455 0.00 0.00 32.73 3.50
796 848 3.160269 CCTTTGGATCAAGCACCTTCTT 58.840 45.455 0.00 0.00 0.00 2.52
850 909 0.693049 GTTTCAGCCTCCTTCCTCCA 59.307 55.000 0.00 0.00 0.00 3.86
1479 1544 3.774959 GACCGGCTGCGTCGATGAT 62.775 63.158 9.31 0.00 29.41 2.45
1483 1548 3.257561 GCTGCGTCGATGATGCGT 61.258 61.111 9.31 0.00 46.39 5.24
1558 1623 1.006400 TGACTCATCTCTCCAGAGCCA 59.994 52.381 0.00 0.00 41.80 4.75
1573 1638 3.841078 CCAGGGATTGGTCAGGGT 58.159 61.111 0.00 0.00 42.41 4.34
1641 1706 1.137825 CACTTCTCTCGCCTCGGTC 59.862 63.158 0.00 0.00 0.00 4.79
1682 1747 1.682451 GGTACCATGGCCGAGCTACA 61.682 60.000 13.04 0.00 0.00 2.74
1683 1748 0.177141 GTACCATGGCCGAGCTACAA 59.823 55.000 13.04 0.00 0.00 2.41
1695 1760 2.166270 GCTACAACAGCTGCTGTCC 58.834 57.895 33.00 14.24 44.62 4.02
1724 1789 4.834453 CTCGGGCCAGCAGCTCAG 62.834 72.222 4.39 0.00 45.13 3.35
1779 1844 1.127343 GCAGTGAGGGAAGGCTAGAT 58.873 55.000 0.00 0.00 0.00 1.98
1797 1862 4.917906 AGATGAGGCCTGTAAAACTCTT 57.082 40.909 12.00 0.00 0.00 2.85
1899 1964 1.132453 CATGACATTGCCAGTGAGCTG 59.868 52.381 0.00 0.00 42.22 4.24
1900 1965 1.239296 TGACATTGCCAGTGAGCTGC 61.239 55.000 0.00 0.00 41.26 5.25
1918 1983 1.303074 CTGGGATCCATGGCATCCG 60.303 63.158 24.90 15.13 40.91 4.18
2202 2267 0.035439 TTCCATCCGAAGCCCTTCAC 60.035 55.000 8.58 0.00 39.46 3.18
2655 2720 1.212751 GGAAGGCGCCAATGTTCAC 59.787 57.895 31.54 13.09 0.00 3.18
2697 2762 3.243336 CGTGGTAGTTGTGCTCTTAGTC 58.757 50.000 0.00 0.00 0.00 2.59
3032 3097 6.915786 AGATCCTTGCTATAACATTTTCCCT 58.084 36.000 0.00 0.00 0.00 4.20
3034 3099 6.773976 TCCTTGCTATAACATTTTCCCTTG 57.226 37.500 0.00 0.00 0.00 3.61
3119 3184 7.287696 ACCTTTTGAATATCATCCCACCATTAC 59.712 37.037 0.00 0.00 0.00 1.89
3333 3398 8.534496 CCCATGGACTAGATTTGAAAGAAATTT 58.466 33.333 15.22 0.00 0.00 1.82
3562 3633 5.856126 TTTCTGTATCCGTTTTAGCACTG 57.144 39.130 0.00 0.00 0.00 3.66
3762 3879 4.461431 AGAATGACATTCAGCTCAAATGCA 59.539 37.500 26.05 14.05 41.71 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 8.287439 TGGGTTTATTTATCACACAATCGAAT 57.713 30.769 0.00 0.00 0.00 3.34
104 105 7.445121 TGCATTTTGGGTTTATTTATCACACA 58.555 30.769 0.00 0.00 0.00 3.72
106 107 7.675062 ACTGCATTTTGGGTTTATTTATCACA 58.325 30.769 0.00 0.00 0.00 3.58
156 157 8.792633 CAAAGTTGTATGGTTTTATCTTGAGGA 58.207 33.333 0.00 0.00 0.00 3.71
188 201 2.902484 CGAAACTAAATGCTGCGTTGTC 59.098 45.455 8.03 1.04 0.00 3.18
194 207 2.729156 GCCAGTCGAAACTAAATGCTGC 60.729 50.000 0.00 0.00 33.25 5.25
195 208 2.744202 AGCCAGTCGAAACTAAATGCTG 59.256 45.455 0.00 0.00 33.25 4.41
209 222 1.610886 GGGTTTCACCACTAGCCAGTC 60.611 57.143 0.00 0.00 41.02 3.51
213 226 3.359695 TTATGGGTTTCACCACTAGCC 57.640 47.619 0.00 0.00 44.72 3.93
233 253 9.821240 TGCTATCCATATACCAAAACCATAAAT 57.179 29.630 0.00 0.00 0.00 1.40
234 254 9.647918 TTGCTATCCATATACCAAAACCATAAA 57.352 29.630 0.00 0.00 0.00 1.40
236 256 8.444783 ACTTGCTATCCATATACCAAAACCATA 58.555 33.333 0.00 0.00 0.00 2.74
237 257 7.297614 ACTTGCTATCCATATACCAAAACCAT 58.702 34.615 0.00 0.00 0.00 3.55
240 260 9.516314 GAAAACTTGCTATCCATATACCAAAAC 57.484 33.333 0.00 0.00 0.00 2.43
241 261 9.249053 TGAAAACTTGCTATCCATATACCAAAA 57.751 29.630 0.00 0.00 0.00 2.44
242 262 8.815565 TGAAAACTTGCTATCCATATACCAAA 57.184 30.769 0.00 0.00 0.00 3.28
243 263 8.849168 CATGAAAACTTGCTATCCATATACCAA 58.151 33.333 0.00 0.00 0.00 3.67
244 264 7.040478 GCATGAAAACTTGCTATCCATATACCA 60.040 37.037 0.00 0.00 0.00 3.25
245 265 7.040478 TGCATGAAAACTTGCTATCCATATACC 60.040 37.037 0.00 0.00 0.00 2.73
246 266 7.874940 TGCATGAAAACTTGCTATCCATATAC 58.125 34.615 0.00 0.00 0.00 1.47
248 268 6.964807 TGCATGAAAACTTGCTATCCATAT 57.035 33.333 0.00 0.00 0.00 1.78
252 272 4.500375 GGGATGCATGAAAACTTGCTATCC 60.500 45.833 2.46 18.67 35.86 2.59
256 276 2.532843 AGGGATGCATGAAAACTTGCT 58.467 42.857 2.46 0.00 0.00 3.91
257 277 3.256558 GAAGGGATGCATGAAAACTTGC 58.743 45.455 2.46 0.00 0.00 4.01
259 279 4.529377 ACATGAAGGGATGCATGAAAACTT 59.471 37.500 2.46 0.52 43.43 2.66
263 283 3.699413 TGACATGAAGGGATGCATGAAA 58.301 40.909 2.46 0.00 43.43 2.69
266 286 4.665833 ATTTGACATGAAGGGATGCATG 57.334 40.909 2.46 0.00 45.56 4.06
267 287 5.424757 CAAATTTGACATGAAGGGATGCAT 58.575 37.500 13.08 0.00 0.00 3.96
270 290 5.410355 ACCAAATTTGACATGAAGGGATG 57.590 39.130 19.86 0.57 0.00 3.51
271 291 5.543405 TGAACCAAATTTGACATGAAGGGAT 59.457 36.000 19.86 0.00 0.00 3.85
272 292 4.898265 TGAACCAAATTTGACATGAAGGGA 59.102 37.500 19.86 0.00 0.00 4.20
273 293 5.212532 TGAACCAAATTTGACATGAAGGG 57.787 39.130 19.86 1.86 0.00 3.95
274 294 5.870978 GGATGAACCAAATTTGACATGAAGG 59.129 40.000 19.86 2.60 38.79 3.46
275 295 5.870978 GGGATGAACCAAATTTGACATGAAG 59.129 40.000 19.86 3.43 41.20 3.02
307 359 9.586150 CAGCTAAAACGTGCTAATAATATCAAG 57.414 33.333 0.00 0.00 37.81 3.02
318 370 1.000060 ACGGACAGCTAAAACGTGCTA 60.000 47.619 0.00 0.00 37.81 3.49
319 371 0.249741 ACGGACAGCTAAAACGTGCT 60.250 50.000 4.46 0.00 40.54 4.40
324 376 5.865552 TCAGTACATAACGGACAGCTAAAAC 59.134 40.000 0.00 0.00 0.00 2.43
325 377 6.028146 TCAGTACATAACGGACAGCTAAAA 57.972 37.500 0.00 0.00 0.00 1.52
330 382 5.796350 AATTTCAGTACATAACGGACAGC 57.204 39.130 0.00 0.00 31.58 4.40
332 384 9.438228 TTCATAAATTTCAGTACATAACGGACA 57.562 29.630 0.00 0.00 31.58 4.02
335 387 7.855904 GCCTTCATAAATTTCAGTACATAACGG 59.144 37.037 0.00 0.00 0.00 4.44
343 395 6.832520 TGCAAGCCTTCATAAATTTCAGTA 57.167 33.333 0.00 0.00 0.00 2.74
345 397 6.814644 TCAATGCAAGCCTTCATAAATTTCAG 59.185 34.615 0.00 0.00 0.00 3.02
346 398 6.699366 TCAATGCAAGCCTTCATAAATTTCA 58.301 32.000 0.00 0.00 0.00 2.69
347 399 7.599630 TTCAATGCAAGCCTTCATAAATTTC 57.400 32.000 0.00 0.00 0.00 2.17
348 400 9.841295 ATATTCAATGCAAGCCTTCATAAATTT 57.159 25.926 0.00 0.00 0.00 1.82
349 401 9.268268 CATATTCAATGCAAGCCTTCATAAATT 57.732 29.630 0.00 0.00 0.00 1.82
350 402 7.386848 GCATATTCAATGCAAGCCTTCATAAAT 59.613 33.333 5.14 0.00 44.00 1.40
351 403 6.702723 GCATATTCAATGCAAGCCTTCATAAA 59.297 34.615 5.14 0.00 44.00 1.40
352 404 6.218019 GCATATTCAATGCAAGCCTTCATAA 58.782 36.000 5.14 0.00 44.00 1.90
353 405 5.279106 GGCATATTCAATGCAAGCCTTCATA 60.279 40.000 11.69 0.00 46.21 2.15
354 406 4.502604 GGCATATTCAATGCAAGCCTTCAT 60.503 41.667 11.69 0.00 46.21 2.57
357 409 3.464111 GGCATATTCAATGCAAGCCTT 57.536 42.857 11.69 0.00 46.21 4.35
362 414 8.789825 AAATGTTTTAGGCATATTCAATGCAA 57.210 26.923 11.69 0.00 46.21 4.08
382 434 9.584008 AAGCTTATCCAATATCATCTGAAATGT 57.416 29.630 0.00 0.00 0.00 2.71
386 438 9.857656 AAAGAAGCTTATCCAATATCATCTGAA 57.142 29.630 0.00 0.00 0.00 3.02
392 444 8.267183 TCTGTCAAAGAAGCTTATCCAATATCA 58.733 33.333 0.00 0.00 29.54 2.15
396 448 7.951347 AATCTGTCAAAGAAGCTTATCCAAT 57.049 32.000 0.00 0.00 38.79 3.16
450 502 7.099764 GTCTGGACATAGTAACATATGATGGG 58.900 42.308 10.38 0.00 36.76 4.00
457 509 7.712204 TTGACTGTCTGGACATAGTAACATA 57.288 36.000 9.51 0.00 41.01 2.29
494 546 4.038763 CGTATCCAAGCACCCTCATAGTAA 59.961 45.833 0.00 0.00 0.00 2.24
495 547 3.572682 CGTATCCAAGCACCCTCATAGTA 59.427 47.826 0.00 0.00 0.00 1.82
496 548 2.365617 CGTATCCAAGCACCCTCATAGT 59.634 50.000 0.00 0.00 0.00 2.12
497 549 2.365617 ACGTATCCAAGCACCCTCATAG 59.634 50.000 0.00 0.00 0.00 2.23
498 550 2.394632 ACGTATCCAAGCACCCTCATA 58.605 47.619 0.00 0.00 0.00 2.15
499 551 1.204146 ACGTATCCAAGCACCCTCAT 58.796 50.000 0.00 0.00 0.00 2.90
500 552 0.981183 AACGTATCCAAGCACCCTCA 59.019 50.000 0.00 0.00 0.00 3.86
501 553 2.109425 AAACGTATCCAAGCACCCTC 57.891 50.000 0.00 0.00 0.00 4.30
502 554 2.579410 AAAACGTATCCAAGCACCCT 57.421 45.000 0.00 0.00 0.00 4.34
503 555 3.340928 ACTAAAACGTATCCAAGCACCC 58.659 45.455 0.00 0.00 0.00 4.61
504 556 3.373130 GGACTAAAACGTATCCAAGCACC 59.627 47.826 0.00 0.00 0.00 5.01
505 557 3.373130 GGGACTAAAACGTATCCAAGCAC 59.627 47.826 0.00 0.00 32.45 4.40
506 558 3.008157 TGGGACTAAAACGTATCCAAGCA 59.992 43.478 0.00 0.00 32.45 3.91
507 559 3.602483 TGGGACTAAAACGTATCCAAGC 58.398 45.455 0.00 0.00 32.45 4.01
508 560 4.574828 CCATGGGACTAAAACGTATCCAAG 59.425 45.833 2.85 0.00 32.45 3.61
509 561 4.519213 CCATGGGACTAAAACGTATCCAA 58.481 43.478 2.85 0.00 32.45 3.53
510 562 3.118186 CCCATGGGACTAAAACGTATCCA 60.118 47.826 28.27 0.00 37.50 3.41
511 563 3.135167 TCCCATGGGACTAAAACGTATCC 59.865 47.826 30.62 0.00 39.76 2.59
512 564 4.411256 TCCCATGGGACTAAAACGTATC 57.589 45.455 30.62 0.00 39.76 2.24
524 576 3.135167 GGATACGTTTTAGTCCCATGGGA 59.865 47.826 30.62 30.62 42.90 4.37
525 577 3.118186 TGGATACGTTTTAGTCCCATGGG 60.118 47.826 26.30 26.30 42.51 4.00
526 578 4.145365 TGGATACGTTTTAGTCCCATGG 57.855 45.455 4.14 4.14 42.51 3.66
527 579 6.503589 TTTTGGATACGTTTTAGTCCCATG 57.496 37.500 0.00 0.00 42.51 3.66
528 580 6.887545 TGATTTTGGATACGTTTTAGTCCCAT 59.112 34.615 0.00 0.00 42.51 4.00
529 581 6.239396 TGATTTTGGATACGTTTTAGTCCCA 58.761 36.000 0.00 0.00 42.51 4.37
530 582 6.746745 TGATTTTGGATACGTTTTAGTCCC 57.253 37.500 0.00 0.00 42.51 4.46
531 583 7.813645 ACTTGATTTTGGATACGTTTTAGTCC 58.186 34.615 0.00 0.00 42.51 3.85
537 589 9.840427 CTCAATAACTTGATTTTGGATACGTTT 57.160 29.630 0.00 0.00 40.52 3.60
538 590 7.968405 GCTCAATAACTTGATTTTGGATACGTT 59.032 33.333 0.00 0.00 40.52 3.99
539 591 7.120579 TGCTCAATAACTTGATTTTGGATACGT 59.879 33.333 0.00 0.00 40.52 3.57
540 592 7.471721 TGCTCAATAACTTGATTTTGGATACG 58.528 34.615 0.00 0.00 40.52 3.06
541 593 9.807649 AATGCTCAATAACTTGATTTTGGATAC 57.192 29.630 0.00 0.00 40.52 2.24
558 610 8.424133 GGGTTTGAAGGATAATAAATGCTCAAT 58.576 33.333 0.00 0.00 0.00 2.57
559 611 7.619302 AGGGTTTGAAGGATAATAAATGCTCAA 59.381 33.333 0.00 0.00 0.00 3.02
560 612 7.125391 AGGGTTTGAAGGATAATAAATGCTCA 58.875 34.615 0.00 0.00 0.00 4.26
561 613 7.588497 AGGGTTTGAAGGATAATAAATGCTC 57.412 36.000 0.00 0.00 0.00 4.26
562 614 7.619302 TGAAGGGTTTGAAGGATAATAAATGCT 59.381 33.333 0.00 0.00 0.00 3.79
563 615 7.781056 TGAAGGGTTTGAAGGATAATAAATGC 58.219 34.615 0.00 0.00 0.00 3.56
566 618 9.768215 AGATTGAAGGGTTTGAAGGATAATAAA 57.232 29.630 0.00 0.00 0.00 1.40
569 621 8.781951 TCTAGATTGAAGGGTTTGAAGGATAAT 58.218 33.333 0.00 0.00 0.00 1.28
570 622 8.158025 TCTAGATTGAAGGGTTTGAAGGATAA 57.842 34.615 0.00 0.00 0.00 1.75
571 623 7.749377 TCTAGATTGAAGGGTTTGAAGGATA 57.251 36.000 0.00 0.00 0.00 2.59
572 624 6.642733 TCTAGATTGAAGGGTTTGAAGGAT 57.357 37.500 0.00 0.00 0.00 3.24
573 625 6.044404 AGTTCTAGATTGAAGGGTTTGAAGGA 59.956 38.462 0.00 0.00 0.00 3.36
574 626 6.241645 AGTTCTAGATTGAAGGGTTTGAAGG 58.758 40.000 0.00 0.00 0.00 3.46
575 627 6.091441 CGAGTTCTAGATTGAAGGGTTTGAAG 59.909 42.308 0.00 0.00 0.00 3.02
576 628 5.932303 CGAGTTCTAGATTGAAGGGTTTGAA 59.068 40.000 0.00 0.00 0.00 2.69
577 629 5.479306 CGAGTTCTAGATTGAAGGGTTTGA 58.521 41.667 0.00 0.00 0.00 2.69
578 630 4.093556 GCGAGTTCTAGATTGAAGGGTTTG 59.906 45.833 0.00 0.00 0.00 2.93
579 631 4.254492 GCGAGTTCTAGATTGAAGGGTTT 58.746 43.478 0.00 0.00 0.00 3.27
580 632 3.260884 TGCGAGTTCTAGATTGAAGGGTT 59.739 43.478 0.00 0.00 0.00 4.11
581 633 2.832129 TGCGAGTTCTAGATTGAAGGGT 59.168 45.455 0.00 0.00 0.00 4.34
582 634 3.526931 TGCGAGTTCTAGATTGAAGGG 57.473 47.619 0.00 0.00 0.00 3.95
583 635 4.269603 CACATGCGAGTTCTAGATTGAAGG 59.730 45.833 0.00 0.00 0.00 3.46
584 636 4.867047 ACACATGCGAGTTCTAGATTGAAG 59.133 41.667 0.00 0.00 0.00 3.02
585 637 4.820897 ACACATGCGAGTTCTAGATTGAA 58.179 39.130 0.00 0.00 0.00 2.69
586 638 4.456280 ACACATGCGAGTTCTAGATTGA 57.544 40.909 0.00 0.00 0.00 2.57
587 639 6.647212 TTAACACATGCGAGTTCTAGATTG 57.353 37.500 0.00 0.00 0.00 2.67
588 640 7.097192 TCTTTAACACATGCGAGTTCTAGATT 58.903 34.615 0.00 0.00 0.00 2.40
589 641 6.631016 TCTTTAACACATGCGAGTTCTAGAT 58.369 36.000 0.00 0.00 0.00 1.98
590 642 6.020971 TCTTTAACACATGCGAGTTCTAGA 57.979 37.500 0.00 0.00 0.00 2.43
591 643 6.586463 TCTTCTTTAACACATGCGAGTTCTAG 59.414 38.462 0.00 0.00 0.00 2.43
592 644 6.452242 TCTTCTTTAACACATGCGAGTTCTA 58.548 36.000 0.00 0.00 0.00 2.10
593 645 5.297547 TCTTCTTTAACACATGCGAGTTCT 58.702 37.500 0.00 0.00 0.00 3.01
594 646 5.389935 CCTCTTCTTTAACACATGCGAGTTC 60.390 44.000 0.00 0.00 0.00 3.01
595 647 4.452455 CCTCTTCTTTAACACATGCGAGTT 59.548 41.667 0.00 0.00 0.00 3.01
596 648 3.997021 CCTCTTCTTTAACACATGCGAGT 59.003 43.478 0.00 0.00 0.00 4.18
597 649 3.181516 GCCTCTTCTTTAACACATGCGAG 60.182 47.826 0.00 0.00 0.00 5.03
598 650 2.742053 GCCTCTTCTTTAACACATGCGA 59.258 45.455 0.00 0.00 0.00 5.10
599 651 2.483877 TGCCTCTTCTTTAACACATGCG 59.516 45.455 0.00 0.00 0.00 4.73
600 652 4.708726 ATGCCTCTTCTTTAACACATGC 57.291 40.909 0.00 0.00 0.00 4.06
601 653 9.079833 CATTTAATGCCTCTTCTTTAACACATG 57.920 33.333 0.00 0.00 0.00 3.21
602 654 9.023962 TCATTTAATGCCTCTTCTTTAACACAT 57.976 29.630 0.00 0.00 0.00 3.21
603 655 8.402798 TCATTTAATGCCTCTTCTTTAACACA 57.597 30.769 0.00 0.00 0.00 3.72
604 656 9.294030 CATCATTTAATGCCTCTTCTTTAACAC 57.706 33.333 0.00 0.00 0.00 3.32
605 657 9.241919 TCATCATTTAATGCCTCTTCTTTAACA 57.758 29.630 0.00 0.00 0.00 2.41
606 658 9.727627 CTCATCATTTAATGCCTCTTCTTTAAC 57.272 33.333 0.00 0.00 0.00 2.01
607 659 9.685276 TCTCATCATTTAATGCCTCTTCTTTAA 57.315 29.630 0.00 0.00 0.00 1.52
608 660 9.334947 CTCTCATCATTTAATGCCTCTTCTTTA 57.665 33.333 0.00 0.00 0.00 1.85
609 661 8.051535 TCTCTCATCATTTAATGCCTCTTCTTT 58.948 33.333 0.00 0.00 0.00 2.52
610 662 7.571919 TCTCTCATCATTTAATGCCTCTTCTT 58.428 34.615 0.00 0.00 0.00 2.52
611 663 7.070946 TCTCTCTCATCATTTAATGCCTCTTCT 59.929 37.037 0.00 0.00 0.00 2.85
612 664 7.215789 TCTCTCTCATCATTTAATGCCTCTTC 58.784 38.462 0.00 0.00 0.00 2.87
613 665 7.134362 TCTCTCTCATCATTTAATGCCTCTT 57.866 36.000 0.00 0.00 0.00 2.85
614 666 6.239657 CCTCTCTCTCATCATTTAATGCCTCT 60.240 42.308 0.00 0.00 0.00 3.69
615 667 5.933463 CCTCTCTCTCATCATTTAATGCCTC 59.067 44.000 0.00 0.00 0.00 4.70
616 668 5.221884 CCCTCTCTCTCATCATTTAATGCCT 60.222 44.000 0.00 0.00 0.00 4.75
617 669 5.002516 CCCTCTCTCTCATCATTTAATGCC 58.997 45.833 0.00 0.00 0.00 4.40
618 670 4.455190 GCCCTCTCTCTCATCATTTAATGC 59.545 45.833 0.00 0.00 0.00 3.56
619 671 5.867330 AGCCCTCTCTCTCATCATTTAATG 58.133 41.667 0.00 0.00 0.00 1.90
620 672 7.623999 TTAGCCCTCTCTCTCATCATTTAAT 57.376 36.000 0.00 0.00 0.00 1.40
621 673 7.623999 ATTAGCCCTCTCTCTCATCATTTAA 57.376 36.000 0.00 0.00 0.00 1.52
622 674 7.730332 TGTATTAGCCCTCTCTCTCATCATTTA 59.270 37.037 0.00 0.00 0.00 1.40
623 675 6.556495 TGTATTAGCCCTCTCTCTCATCATTT 59.444 38.462 0.00 0.00 0.00 2.32
624 676 6.080682 TGTATTAGCCCTCTCTCTCATCATT 58.919 40.000 0.00 0.00 0.00 2.57
625 677 5.649265 TGTATTAGCCCTCTCTCTCATCAT 58.351 41.667 0.00 0.00 0.00 2.45
626 678 5.066913 TGTATTAGCCCTCTCTCTCATCA 57.933 43.478 0.00 0.00 0.00 3.07
627 679 7.896383 ATATGTATTAGCCCTCTCTCTCATC 57.104 40.000 0.00 0.00 0.00 2.92
628 680 8.677870 AAATATGTATTAGCCCTCTCTCTCAT 57.322 34.615 0.00 0.00 0.00 2.90
629 681 8.497910 AAAATATGTATTAGCCCTCTCTCTCA 57.502 34.615 0.00 0.00 0.00 3.27
631 683 9.608718 ACTAAAATATGTATTAGCCCTCTCTCT 57.391 33.333 0.00 0.00 33.39 3.10
674 726 8.924303 AGGACTAGTTTTGAGGCTAAAATTTTT 58.076 29.630 9.06 0.00 32.71 1.94
675 727 8.478775 AGGACTAGTTTTGAGGCTAAAATTTT 57.521 30.769 8.75 8.75 32.71 1.82
676 728 9.232473 CTAGGACTAGTTTTGAGGCTAAAATTT 57.768 33.333 0.00 0.00 32.71 1.82
677 729 7.337184 GCTAGGACTAGTTTTGAGGCTAAAATT 59.663 37.037 0.00 1.16 35.65 1.82
678 730 6.824196 GCTAGGACTAGTTTTGAGGCTAAAAT 59.176 38.462 0.00 0.00 35.65 1.82
679 731 6.171213 GCTAGGACTAGTTTTGAGGCTAAAA 58.829 40.000 0.00 0.00 35.65 1.52
680 732 5.338137 GGCTAGGACTAGTTTTGAGGCTAAA 60.338 44.000 0.00 0.00 35.65 1.85
681 733 4.161754 GGCTAGGACTAGTTTTGAGGCTAA 59.838 45.833 0.00 0.00 35.65 3.09
682 734 3.705072 GGCTAGGACTAGTTTTGAGGCTA 59.295 47.826 0.00 0.00 35.65 3.93
683 735 2.502130 GGCTAGGACTAGTTTTGAGGCT 59.498 50.000 0.00 0.00 35.65 4.58
684 736 2.502130 AGGCTAGGACTAGTTTTGAGGC 59.498 50.000 0.00 5.24 35.65 4.70
685 737 4.027437 AGAGGCTAGGACTAGTTTTGAGG 58.973 47.826 0.00 0.00 35.65 3.86
686 738 4.953579 AGAGAGGCTAGGACTAGTTTTGAG 59.046 45.833 0.00 0.00 35.65 3.02
687 739 4.936802 AGAGAGGCTAGGACTAGTTTTGA 58.063 43.478 0.00 0.00 35.65 2.69
688 740 5.669164 AAGAGAGGCTAGGACTAGTTTTG 57.331 43.478 0.00 0.00 35.65 2.44
689 741 6.955267 ACTAAAGAGAGGCTAGGACTAGTTTT 59.045 38.462 0.00 0.00 35.65 2.43
690 742 6.495847 ACTAAAGAGAGGCTAGGACTAGTTT 58.504 40.000 0.00 2.90 35.65 2.66
691 743 6.082228 ACTAAAGAGAGGCTAGGACTAGTT 57.918 41.667 0.00 0.00 35.65 2.24
692 744 5.192121 TGACTAAAGAGAGGCTAGGACTAGT 59.808 44.000 0.00 0.00 35.65 2.57
693 745 5.686753 TGACTAAAGAGAGGCTAGGACTAG 58.313 45.833 1.98 1.98 36.29 2.57
694 746 5.398126 CCTGACTAAAGAGAGGCTAGGACTA 60.398 48.000 0.00 0.00 29.08 2.59
695 747 4.532834 CTGACTAAAGAGAGGCTAGGACT 58.467 47.826 0.00 0.00 0.00 3.85
696 748 3.634910 CCTGACTAAAGAGAGGCTAGGAC 59.365 52.174 0.00 0.00 29.08 3.85
697 749 3.528078 TCCTGACTAAAGAGAGGCTAGGA 59.472 47.826 0.00 0.00 32.53 2.94
698 750 3.888930 CTCCTGACTAAAGAGAGGCTAGG 59.111 52.174 0.00 0.00 0.00 3.02
699 751 4.338118 CACTCCTGACTAAAGAGAGGCTAG 59.662 50.000 0.00 0.00 0.00 3.42
700 752 4.274147 CACTCCTGACTAAAGAGAGGCTA 58.726 47.826 0.00 0.00 0.00 3.93
701 753 3.096092 CACTCCTGACTAAAGAGAGGCT 58.904 50.000 0.00 0.00 0.00 4.58
702 754 2.418060 GCACTCCTGACTAAAGAGAGGC 60.418 54.545 0.00 0.00 0.00 4.70
703 755 3.096092 AGCACTCCTGACTAAAGAGAGG 58.904 50.000 0.00 0.00 0.00 3.69
704 756 4.219507 TCAAGCACTCCTGACTAAAGAGAG 59.780 45.833 0.00 0.00 0.00 3.20
705 757 4.152647 TCAAGCACTCCTGACTAAAGAGA 58.847 43.478 0.00 0.00 0.00 3.10
706 758 4.527509 TCAAGCACTCCTGACTAAAGAG 57.472 45.455 0.00 0.00 0.00 2.85
707 759 4.955811 TTCAAGCACTCCTGACTAAAGA 57.044 40.909 0.00 0.00 0.00 2.52
708 760 5.059833 AGTTTCAAGCACTCCTGACTAAAG 58.940 41.667 0.00 0.00 0.00 1.85
709 761 5.036117 AGTTTCAAGCACTCCTGACTAAA 57.964 39.130 0.00 0.00 0.00 1.85
710 762 4.689612 AGTTTCAAGCACTCCTGACTAA 57.310 40.909 0.00 0.00 0.00 2.24
711 763 4.689612 AAGTTTCAAGCACTCCTGACTA 57.310 40.909 0.00 0.00 0.00 2.59
712 764 3.567478 AAGTTTCAAGCACTCCTGACT 57.433 42.857 0.00 0.00 0.00 3.41
713 765 4.816925 ACTAAAGTTTCAAGCACTCCTGAC 59.183 41.667 0.00 0.00 0.00 3.51
714 766 5.036117 ACTAAAGTTTCAAGCACTCCTGA 57.964 39.130 0.00 0.00 0.00 3.86
715 767 5.059833 AGACTAAAGTTTCAAGCACTCCTG 58.940 41.667 0.00 0.00 0.00 3.86
716 768 5.297569 AGACTAAAGTTTCAAGCACTCCT 57.702 39.130 0.00 0.00 0.00 3.69
717 769 6.378710 AAAGACTAAAGTTTCAAGCACTCC 57.621 37.500 0.00 0.00 0.00 3.85
718 770 9.783256 TTTTAAAGACTAAAGTTTCAAGCACTC 57.217 29.630 0.00 0.00 0.00 3.51
757 809 9.981460 ATCCAAAGGACTATTTTTAGTCTGATT 57.019 29.630 11.69 4.07 44.35 2.57
758 810 9.620259 GATCCAAAGGACTATTTTTAGTCTGAT 57.380 33.333 11.69 7.35 44.35 2.90
759 811 8.602424 TGATCCAAAGGACTATTTTTAGTCTGA 58.398 33.333 11.69 3.95 44.35 3.27
760 812 8.792830 TGATCCAAAGGACTATTTTTAGTCTG 57.207 34.615 11.69 4.29 44.35 3.51
761 813 9.454859 CTTGATCCAAAGGACTATTTTTAGTCT 57.545 33.333 11.69 0.00 44.35 3.24
762 814 8.184848 GCTTGATCCAAAGGACTATTTTTAGTC 58.815 37.037 4.87 4.87 44.23 2.59
763 815 7.669722 TGCTTGATCCAAAGGACTATTTTTAGT 59.330 33.333 0.00 0.00 32.98 2.24
764 816 7.970614 GTGCTTGATCCAAAGGACTATTTTTAG 59.029 37.037 9.37 0.00 43.09 1.85
765 817 7.093945 GGTGCTTGATCCAAAGGACTATTTTTA 60.094 37.037 14.38 0.00 45.04 1.52
766 818 6.295292 GGTGCTTGATCCAAAGGACTATTTTT 60.295 38.462 14.38 0.00 45.04 1.94
767 819 5.185828 GGTGCTTGATCCAAAGGACTATTTT 59.814 40.000 14.38 0.00 45.04 1.82
768 820 4.706962 GGTGCTTGATCCAAAGGACTATTT 59.293 41.667 14.38 0.00 45.04 1.40
769 821 4.018050 AGGTGCTTGATCCAAAGGACTATT 60.018 41.667 14.38 2.40 45.04 1.73
770 822 3.525199 AGGTGCTTGATCCAAAGGACTAT 59.475 43.478 14.38 4.49 45.04 2.12
771 823 2.912956 AGGTGCTTGATCCAAAGGACTA 59.087 45.455 14.38 0.00 45.04 2.59
772 824 1.707427 AGGTGCTTGATCCAAAGGACT 59.293 47.619 14.38 2.22 45.04 3.85
773 825 2.206576 AGGTGCTTGATCCAAAGGAC 57.793 50.000 8.42 8.42 44.99 3.85
774 826 2.376518 AGAAGGTGCTTGATCCAAAGGA 59.623 45.455 0.00 0.00 35.55 3.36
775 827 2.800250 AGAAGGTGCTTGATCCAAAGG 58.200 47.619 0.00 0.00 0.00 3.11
776 828 4.038402 ACAAAGAAGGTGCTTGATCCAAAG 59.962 41.667 0.00 0.00 0.00 2.77
777 829 3.960102 ACAAAGAAGGTGCTTGATCCAAA 59.040 39.130 0.00 0.00 0.00 3.28
778 830 3.565307 ACAAAGAAGGTGCTTGATCCAA 58.435 40.909 0.00 0.00 0.00 3.53
779 831 3.149196 GACAAAGAAGGTGCTTGATCCA 58.851 45.455 0.00 0.00 0.00 3.41
780 832 2.489722 GGACAAAGAAGGTGCTTGATCC 59.510 50.000 0.00 0.00 0.00 3.36
781 833 3.149196 TGGACAAAGAAGGTGCTTGATC 58.851 45.455 0.00 0.00 0.00 2.92
782 834 3.152341 CTGGACAAAGAAGGTGCTTGAT 58.848 45.455 0.00 0.00 0.00 2.57
783 835 2.092429 ACTGGACAAAGAAGGTGCTTGA 60.092 45.455 0.00 0.00 0.00 3.02
784 836 2.301346 ACTGGACAAAGAAGGTGCTTG 58.699 47.619 0.00 0.00 0.00 4.01
785 837 2.736670 ACTGGACAAAGAAGGTGCTT 57.263 45.000 0.00 0.00 0.00 3.91
786 838 2.706190 AGTACTGGACAAAGAAGGTGCT 59.294 45.455 0.00 0.00 0.00 4.40
787 839 3.067833 GAGTACTGGACAAAGAAGGTGC 58.932 50.000 0.00 0.00 0.00 5.01
788 840 3.243771 ACGAGTACTGGACAAAGAAGGTG 60.244 47.826 12.28 0.00 0.00 4.00
789 841 2.963782 ACGAGTACTGGACAAAGAAGGT 59.036 45.455 12.28 0.00 0.00 3.50
790 842 3.662247 ACGAGTACTGGACAAAGAAGG 57.338 47.619 12.28 0.00 0.00 3.46
791 843 6.090898 CCAAATACGAGTACTGGACAAAGAAG 59.909 42.308 12.28 0.00 0.00 2.85
792 844 5.929992 CCAAATACGAGTACTGGACAAAGAA 59.070 40.000 12.28 0.00 0.00 2.52
793 845 5.475719 CCAAATACGAGTACTGGACAAAGA 58.524 41.667 12.28 0.00 0.00 2.52
796 848 3.833650 TCCCAAATACGAGTACTGGACAA 59.166 43.478 12.28 0.00 0.00 3.18
1452 1517 3.699894 CAGCCGGTCCTGAGCAGT 61.700 66.667 1.90 0.00 34.77 4.40
1558 1623 1.384191 GCAACCCTGACCAATCCCT 59.616 57.895 0.00 0.00 0.00 4.20
1573 1638 3.801129 TGTGAAACAGACGCGCAA 58.199 50.000 5.73 0.00 45.67 4.85
1662 1727 1.382009 TAGCTCGGCCATGGTACCA 60.382 57.895 18.99 18.99 0.00 3.25
1682 1747 0.742281 CGCATAGGACAGCAGCTGTT 60.742 55.000 28.84 16.67 45.44 3.16
1695 1760 2.240500 GCCCGAGACAAGCGCATAG 61.241 63.158 11.47 0.19 0.00 2.23
1724 1789 4.388499 ACGTCCACATGGCCGGAC 62.388 66.667 15.55 15.55 46.88 4.79
1726 1791 4.697756 ACACGTCCACATGGCCGG 62.698 66.667 6.29 0.00 41.45 6.13
1779 1844 2.708861 TCCAAGAGTTTTACAGGCCTCA 59.291 45.455 0.00 0.00 0.00 3.86
1797 1862 2.364632 CCAGAACGCACCATATTTCCA 58.635 47.619 0.00 0.00 0.00 3.53
1899 1964 1.605738 GGATGCCATGGATCCCAGC 60.606 63.158 18.40 10.01 36.75 4.85
1900 1965 1.303074 CGGATGCCATGGATCCCAG 60.303 63.158 25.39 15.33 36.75 4.45
2120 2185 6.499699 AGCCACAAGATCATAAGAGATATCCA 59.500 38.462 0.00 0.00 0.00 3.41
2202 2267 7.095060 CCCAAACCAATCATATCGATGTAGAAG 60.095 40.741 8.54 1.20 33.40 2.85
2655 2720 5.463392 CACGTTGAATGAGGTACTATCCATG 59.537 44.000 0.00 0.00 41.55 3.66
2697 2762 1.652124 GAACTGATGCGCTGCAATTTG 59.348 47.619 9.73 0.00 43.62 2.32
3004 3069 6.874288 AAATGTTATAGCAAGGATCTCTGC 57.126 37.500 10.48 10.48 0.00 4.26
3032 3097 0.537188 TTTTTGTTGGGCGCTTCCAA 59.463 45.000 13.35 13.35 43.82 3.53
3034 3099 1.877637 AATTTTTGTTGGGCGCTTCC 58.122 45.000 7.64 0.33 0.00 3.46
3138 3203 6.849697 TGAGTAGAACCCAAGGTTATGGATAT 59.150 38.462 3.94 0.00 46.95 1.63
3149 3214 3.529533 CTGCATCTGAGTAGAACCCAAG 58.470 50.000 0.00 0.00 36.32 3.61
3333 3398 8.092687 GTGGAGAAACAACTAAAGTATACCTGA 58.907 37.037 0.00 0.00 0.00 3.86
3418 3483 8.600625 TGCATAGTTCAAACTTATGTAACGATC 58.399 33.333 0.00 0.00 40.37 3.69



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.